Loss of microbial diversity and pathogen domination of the gut microbiota in critically ill patients

Ravi, Anuradha, Halstead, Fenella D, Bamford, Amy, Casey, Anna, Thomson, Nicholas M, van Schaik, Willem, Snelson, Catherine, Goulden, Robert, Foster-Nyarko, Ebenezer, Savva, George M, Whitehouse, Tony, Pallen, Mark J ORCID: https://orcid.org/0000-0003-1807-3657 and Oppenheim, Beryl A (2019) Loss of microbial diversity and pathogen domination of the gut microbiota in critically ill patients. Microbial Genomics, 5 (9). ISSN 2057-5858

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Abstract

Among long-stay critically ill patients in the adult intensive care unit (ICU), there are often marked changes in the complexity of the gut microbiota. However, it remains unclear whether such patients might benefit from enhanced surveillance or from interventions targeting the gut microbiota or the pathogens therein. We therefore undertook a prospective observational study of 24 ICU patients, in which serial faecal samples were subjected to shotgun metagenomic sequencing, phylogenetic profiling and microbial genome analyses. Two-thirds of the patients experienced a marked drop in gut microbial diversity (to an inverse Simpson's index of <4) at some stage during their stay in the ICU, often accompanied by the absence or loss of potentially beneficial bacteria. Intravenous administration of the broad-spectrum antimicrobial agent meropenem was significantly associated with loss of gut microbial diversity, but the administration of other antibiotics, including piperacillin/tazobactam, failed to trigger statistically detectable changes in microbial diversity. In three-quarters of ICU patients, we documented episodes of gut domination by pathogenic strains, with evidence of cryptic nosocomial transmission of Enterococcus faecium. In some patients, we also saw an increase in the relative abundance of apparent commensal organisms in the gut microbiome, including the archaeal species Methanobrevibacter smithii. In conclusion, we have documented a dramatic absence of microbial diversity and pathogen domination of the gut microbiota in a high proportion of critically ill patients using shotgun metagenomics.

Item Type:	Article
Faculty \ School:	Faculty of Medicine and Health Sciences > Norwich Medical School Faculty of Medicine and Health Sciences > School of Health Sciences Faculty of Science > School of Biological Sciences
UEA Research Groups:	Faculty of Science > Research Groups > Norwich Epidemiology Centre Faculty of Medicine and Health Sciences > Research Groups > Norwich Epidemiology Centre
Depositing User:	LivePure Connector
Date Deposited:	02 Oct 2019 11:30
Last Modified:	03 Dec 2023 02:44
URI:	https://ueaeprints.uea.ac.uk/id/eprint/72452
DOI:	10.1099/mgen.0.000293

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